FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

被引：293

作者：

dos Santos, Gilberto ^{[1
]}

Schroeder, Andrew J. ^{[1
]}

Goodman, Joshua L. ^{[2
]}

Strelets, Victor B. ^{[2
]}

Crosby, Madeline A. ^{[1
]}

Thurmond, Jim ^{[2
]}

Emmert, David B. ^{[1
]}

Gelbart, William M. ^{[1
]}

机构：

[1] Harvard Univ, Biol Labs, Cambridge, MA 02138 USA

[2] Indiana Univ, Dept Biol, Bloomington, IN 47405 USA

来源：

NUCLEIC ACIDS RESEARCH | 2015年 / 43卷 / D1期

基金：

美国国家卫生研究院; 英国医学研究理事会;

关键词：

SEQUENCE; GENERATION; BROWSER;

D O I：

10.1093/nar/gku1099

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Release 6, the latest reference genome assembly of the fruit fly Drosophila melanogaster, was released by the Berkeley Drosophila Genome Project in 2014; it replaces their previous Release 5 genome assembly, which had been the reference genome assembly for over 7 years. With the enormous amount of information now attached to the D. melanogaster genome in public repositories and individual laboratories, the replacement of the previous assembly by the new one is a major event requiring careful migration of annotations and genome-anchored data to the new, improved assembly. In this report, we describe the attributes of the new Release 6 reference genome assembly, the migration of FlyBase genome annotations to this new assembly, how genome features on this new assembly can be viewed in FlyBase (http://flybase.org) and how users can convert coordinates for their own data to the corresponding Release 6 coordinates.

引用

页码：D690 / D697

页数：8

共 24 条

[11] The developmental transcriptome of Drosophila melanogaster
Graveley, Brenton R.
Brooks, Angela N.
Carlson, JosephW.
Duff, Michael O.
Landolin, Jane M.
Yang, Li
Artieri, Carlo G.
van Baren, Marijke J.
Boley, Nathan
Booth, Benjamin W.
Brown, James B.
Cherbas, Lucy
Davis, Carrie A.
Dobin, Alex
Li, Renhua
Lin, Wei
Malone, John H.
Mattiuzzo, Nicolas R.
Miller, David
Sturgill, David
Tuch, Brian B.
Zaleski, Chris
Zhang, Dayu
Blanchette, Marco
Dudoit, Sandrine
Eads, Brian
Green, Richard E.
Hammonds, Ann
Jiang, Lichun
Kapranov, Phil
Langton, Laura
Perrimon, Norbert
Sandler, Jeremy E.
Wan, Kenneth H.
Willingham, Aarron
Zhang, Yu
Zou, Yi
Andrews, Justen
Bickel, Peter J.
Brenner, Steven E.
Brent, Michael R.
Cherbas, Peter
Gingeras, Thomas R.
Hoskins, Roger A.
Kaufman, Thomas C.
Oliver, Brian
Celniker, Susan E.
[J]. NATURE, 2011, 471 (7339) : 473 - 479
[12] Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster
He, Bing
Caudy, Amy
Parsons, Lance
Rosebrock, Adam
Pane, Attilio
Raj, Sandeep
Wieschaus, Eric
[J]. GENOME RESEARCH, 2012, 22 (12) : 2507 - 2519
[13] Sequence finishing and mapping of Drosophila melanogaster heterochromatin
Hoskins, Roger A.
Carlson, Joseph W.
Kennedy, Cameron
Acevedo, David
Evans-Holm, Martha
Frise, Erwin
Wan, Kenneth H.
Park, Soo
Mendez-Lago, Maria
Rossi, Fabrizio
Villasante, Alfredo
Dimitri, Patrizio
Karpen, Gary H.
Celniker, Susan E.
[J]. SCIENCE, 2007, 316 (5831) : 1625 - 1628
[14] Splign: algorithms for computing spliced alignments with identification of paralogs
Kapustin, Yuri
Souvorov, Alexander
Tatusova, Tatiana
Lipman, David
[J]. BIOLOGY DIRECT, 2008, 3 (1)
[15] The UCSC Genome Browser database: 2014 update
Karolchik, Donna
Barber, Galt P.
Casper, Jonathan
Clawson, Hiram
Cline, Melissa S.
Diekhans, Mark
Dreszer, Timothy R.
Fujita, Pauline A.
Guruvadoo, Luvina
Haeussler, Maximilian
Harte, Rachel A.
Heitner, Steve
Hinrichs, Angie S.
Learned, Katrina
Lee, Brian T.
Li, Chin H.
Raney, Brian J.
Rhead, Brooke
Rosenbloom, Kate R.
Sloan, Cricket A.
Speir, Matthew L.
Zweig, Ann S.
Haussler, David
Kuhn, Robert M.
Kent, W. James
[J]. NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) : D764 - D770
[16] Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, Ali
Williams, Brian A.
McCue, Kenneth
Schaeffer, Lorian
Wold, Barbara
[J]. NATURE METHODS, 2008, 5 (07) : 621 - 628
[17] A Chado case study: an ontology-based modular schema for representing genome-associated biological information
Mungall, Christopher J.
Emmert, David B.
[J]. BIOINFORMATICS, 2007, 23 (13) : I337 - I346
[18] A whole-genome assembly of Drosophila
Myers, EW
Sutton, GG
Delcher, AL
Dew, IM
Fasulo, DP
Flanigan, MJ
Kravitz, SA
Mobarry, CM
Reinert, KHJ
Remington, KA
Anson, EL
Bolanos, RA
Chou, HH
Jordan, CM
Halpern, AL
Lonardi, S
Beasley, EM
Brandon, RC
Chen, L
Dunn, PJ
Lai, ZW
Liang, Y
Nusskern, DR
Zhan, M
Zhang, Q
Zheng, XQ
Rubin, GM
Adams, MD
Venter, JC
[J]. SCIENCE, 2000, 287 (5461) : 2196 - 2204
[19] IMPROVED TOOLS FOR BIOLOGICAL SEQUENCE COMPARISON
PEARSON, WR
LIPMAN, DJ
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1988, 85 (08) : 2444 - 2448
[20] RefSeq: an update on mammalian reference sequences
Pruitt, Kim D.
Brown, Garth R.
Hiatt, Susan M.
Thibaud-Nissen, Francoise
Astashyn, Alexander
Ermolaeva, Olga
Farrell, Catherine M.
Hart, Jennifer
Landrum, Melissa J.
McGarvey, Kelly M.
Murphy, Michael R.
O'Leary, Nuala A.
Pujar, Shashikant
Rajput, Bhanu
Rangwala, Sanjida H.
Riddick, Lillian D.
Shkeda, Andrei
Sun, Hanzhen
Tamez, Pamela
Tully, Raymond E.
Wallin, Craig
Webb, David
Weber, Janet
Wu, Wendy
DiCuccio, Michael
Kitts, Paul
Maglott, Donna R.
Murphy, Terence D.
Ostell, James M.
[J]. NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) : D756 - D763

← 1 2 3 →